untranslated rna

Summary

Summary: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA; (RNA, RIBOSOMAL) and transfer RNA; (RNA, TRANSFER) are also untranslated they are not included here.

Top Publications

  1. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
  2. pmc Regulatory RNAs in bacteria
    Lauren S Waters
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
    Cell 136:615-28. 2009
  3. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
  4. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 129:1311-23. 2007
  5. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
  6. pmc Specific expression of long noncoding RNAs in the mouse brain
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Proc Natl Acad Sci U S A 105:716-21. 2008
  7. ncbi The transcriptional landscape of the mammalian genome
    P Carninci
    Science 309:1559-63. 2005
  8. ncbi An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    N C Lau
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 294:858-62. 2001
  9. pmc Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
    Xiangting Wang
    Howard Hughes Medical Institute
    Nature 454:126-30. 2008
  10. pmc Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Genome Res 18:1433-45. 2008

Detail Information

Publications358 found, 100 shown here

  1. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  2. pmc Regulatory RNAs in bacteria
    Lauren S Waters
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
    Cell 136:615-28. 2009
    ..Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions...
  3. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  4. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 129:1311-23. 2007
    ..Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states...
  5. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
    ..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
  6. pmc Specific expression of long noncoding RNAs in the mouse brain
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Proc Natl Acad Sci U S A 105:716-21. 2008
    ..Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs...
  7. ncbi The transcriptional landscape of the mammalian genome
    P Carninci
    Science 309:1559-63. 2005
    ..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
  8. ncbi An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    N C Lau
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 294:858-62. 2001
    ..The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals...
  9. pmc Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
    Xiangting Wang
    Howard Hughes Medical Institute
    Nature 454:126-30. 2008
    ....
  10. pmc Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Genome Res 18:1433-45. 2008
    ..Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery...
  11. ncbi An extensive class of small RNAs in Caenorhabditis elegans
    R C Lee
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Science 294:862-4. 2001
    ..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse...
  12. ncbi Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  13. ncbi Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
    L Argaman
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, 91120, Jerusalem, Israel
    Curr Biol 11:941-50. 2001
    Small, untranslated RNA molecules were identified initially in bacteria, but examples can be found in all kingdoms of life. These RNAs carry out diverse functions, and many of them are regulators of gene expression...
  14. ncbi microRNAs: tiny regulators with great potential
    V Ambros
    Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
    Cell 107:823-6. 2001
    ..These microRNAs are diverse in sequence and expression patterns, and are evolutionarily widespread, suggesting that they may participate in a wide range of genetic regulatory pathways...
  15. ncbi A system for stable expression of short interfering RNAs in mammalian cells
    Thijn R Brummelkamp
    Division of Molecular Carcinogenesis, Division of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
    Science 296:550-3. 2002
    ..Therefore, the pSUPER vector constitutes a new and powerful system to analyze gene function in a variety of mammalian cell types...
  16. ncbi Evolution and functions of long noncoding RNAs
    Chris P Ponting
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford, OX1 3QX, UK
    Cell 136:629-41. 2009
    ..Here, we review the evolution of lncRNAs and their roles in transcriptional regulation, epigenetic gene regulation, and disease...
  17. pmc Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome
    Jing Zhao
    Howard Hughes Medical Institute, Boston, MA 02115, USA
    Science 322:750-6. 2008
    ..Likewise, PRC2 deficiency compromises Xist up-regulation. Therefore, RepA, together with PRC2, is required for the initiation and spread of XCI. We conclude that a ncRNA cofactor recruits Polycomb complexes to their target locus...
  18. ncbi Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas
    George A Calin
    Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
    Cancer Cell 12:215-29. 2007
    ..Our findings argue that ncRNAs and interaction between noncoding genes are involved in tumorigenesis to a greater extent than previously thought...
  19. ncbi Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA
    Katrin Panzitt
    Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, A 8036 Graz, Austria
    Gastroenterology 132:330-42. 2007
    ..We searched the human genome for novel genes including ncRNAs related to hepatocellular carcinoma (HCC)...
  20. pmc Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    Jasmina Ponjavic
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:556-65. 2007
    ..2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs' functions...
  21. pmc MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
    Hongjae Sunwoo
    Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA
    Genome Res 19:347-59. 2009
    ..Our findings indicate that the MEN epsilon/beta non-coding RNAs are essential structural/organizational components of paraspeckles...
  22. ncbi Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
    Ken C Pang
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
    Trends Genet 22:1-5. 2006
    ..Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function...
  23. pmc Long noncoding RNAs: functional surprises from the RNA world
    Jeremy E Wilusz
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genes Dev 23:1494-504. 2009
    ..It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell...
  24. ncbi Long non-coding RNAs: insights into functions
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Nat Rev Genet 10:155-9. 2009
    ..We also consider the medical implications, and the emerging recognition that any transcript, regardless of coding potential, can have an intrinsic function as an RNA...
  25. ncbi Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes
    Jose Silva
    X Inactivation Group, MRC Clinical Sciences Centre, ICSM, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom
    Dev Cell 4:481-95. 2003
    ..Functional analysis demonstrates that Eed-Enx1 is required to establish methylation of histone H3 at lysine 9 and/or lysine 27 on Xi and that this, in turn, is required to stabilize the Xi chromatin structure...
  26. ncbi Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
    Radha Raman Pandey
    Department of Genetics and Pathology, Dag Hammarskjölds väg 20, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Mol Cell 32:232-46. 2008
    ....
  27. pmc Translational control and target recognition by Escherichia coli small RNAs in vivo
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Nucleic Acids Res 35:1018-37. 2007
    ..We expect our GFP fusion approach to be applicable to sRNA targets of other bacteria, and also demonstrate that Vibrio RyhB sRNA represses a Vibrio sodB fusion when co-expressed in E.coli...
  28. ncbi Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
    A C Bell
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0540, USA
    Nature 405:482-5. 2000
    ..Our results reveal that DNA methylation can control gene expression by modulating enhancer access to the gene promoter through regulation of an enhancer boundary...
  29. ncbi Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript
    Igor Martianov
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Nature 445:666-70. 2007
    ....
  30. ncbi The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
    C J Brown
    Department of Genetics, Stanford University, California 94305
    Cell 71:527-42. 1992
    ..Consistent with this, fluorescence in situ hybridization experiments demonstrate localization of XIST RNA within the nucleus to a position indistinguishable from the X inactivation-associated Barr body...
  31. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
  32. ncbi Noncoding RNA in development
    Paulo P Amaral
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Mamm Genome 19:454-92. 2008
    ....
  33. ncbi A strategy for probing the function of noncoding RNAs finds a repressor of NFAT
    A T Willingham
    Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 309:1570-3. 2005
    ....
  34. ncbi Asymmetry in the assembly of the RNAi enzyme complex
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 115:199-208. 2003
    ..Thus, the common step of RISC assembly is an unexpected source of asymmetry for both siRNA function and miRNA biogenesis...
  35. ncbi Prediction of plant microRNA targets
    Matthew W Rhoades
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
    Cell 110:513-20. 2002
    ..The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages...
  36. pmc Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    Jasmina Ponjavic
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000617. 2009
    ....
  37. ncbi Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi
    Thomas A Volpe
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA
    Science 297:1833-7. 2002
    ..We propose that double-stranded RNA arising from centromeric repeats targets formation and maintenance of heterochromatin through RNAi...
  38. pmc Effect of RyhB small RNA on global iron use in Escherichia coli
    Eric Massé
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    J Bacteriol 187:6962-71. 2005
    ..Our results demonstrate the broad effects of a single noncoding RNA on iron homeostasis...
  39. ncbi An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes
    Jörgen Johansson
    Unité des Interactions Bactéries Cellules, Institut Pasteur, 28, rue du Docteur Roux, 75724 Cedex 15, Paris, France
    Cell 110:551-61. 2002
    ..Strikingly, when the DNA corresponding to the UTR was fused to gfp in E. coli, bacteria became fluorescent at 37 degrees C, but not at 30 degrees C. This mechanism of posttranscriptional thermoregulation may have important applications...
  40. pmc The imprinted H19 noncoding RNA is a primary microRNA precursor
    Xuezhong Cai
    Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    RNA 13:313-6. 2007
    ..These data demonstrate that H19 can function as a primary microRNA precursor and suggest that H19 expression results in the post-transcriptional downregulation of specific mRNAs during vertebrate development...
  41. pmc Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence
    Gilly Padalon-Brauch
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, 91120, Jerusalem, Israel
    Nucleic Acids Res 36:1913-27. 2008
    ..Our study suggests that the island encoded sRNA genes play an important role within the network that regulates bacterial adaptation to environmental changes and stress conditions and thus controls virulence...
  42. ncbi A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation
    A Wutz
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Mol Cell 5:695-705. 2000
    ..Xist had to be activated within 48 hr of differentiation to effect silencing, suggesting that reversible repression by Xist is a required initiation step that might occur during normal X inactivation in female cells...
  43. ncbi Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    Nat Struct Mol Biol 16:840-6. 2009
    ..The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria...
  44. ncbi Chromosomal silencing and localization are mediated by different domains of Xist RNA
    Anton Wutz
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 30:167-74. 2002
    ..Association of Xist RNA with chromatin is mediated by functionally redundant sequences that act cooperatively and are dispersed throughout the remainder of Xist but show little or no homology...
  45. pmc Identification of small RNAs in Mycobacterium tuberculosis
    Kristine B Arnvig
    Division of Mycobacterial Research, MRC National Institute for Medical Research, London NW7 1AA, UK
    Mol Microbiol 73:397-408. 2009
    ..This is the first experimental evidence of sRNAs in M. tuberculosis and it will be important to consider the potential influence of sRNA regulation when studying the transcriptome and the proteome of M. tuberculosis during infection...
  46. pmc Rfam: an RNA family database
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:439-41. 2003
    ..wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database...
  47. pmc SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay
    Kai Papenfort
    Max Planck Institute for Infection Biology, Chariteplatz 1, 10117 Berlin, Germany
    Mol Microbiol 62:1674-88. 2006
    ..In unstressed bacterial cells, the two oE-dependent small RNAs function within a surveillance loop to maintain envelope homeostasis and to achieve autoregulation of oE...
  48. ncbi Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus
    Thean Hock Tang
    Institute for Research in Molecular Medicine, University Sains Malaysia Health Campus, 16150 Kubang Kerian, Kelatan, Malaysia
    Mol Microbiol 55:469-81. 2005
    ..In conclusion, this is the first report of stably expressed antisense RNAs in an archaeal species and it raises the prospect that antisense-based mechanisms are also used widely in Archaea to regulate gene expression...
  49. pmc The H19 non-coding RNA is essential for human tumor growth
    Imad J Matouk
    Department of Biological Chemistry, Institute of Life Sciences, Hebrew University, Jerusalem, Israel
    PLoS ONE 2:e845. 2007
    ..Moreover, H19 is highly expressed in liver metastasis derived from a range of carcinomas. The objective of this study is to explore the role of H19 in carcinogenesis, and to determine its identification as an anti-tumor target...
  50. pmc Small untranslated RNA antitoxin in Bacillus subtilis
    Jessica M Silvaggi
    Department of Molecular and Cellular Biology, The Biological Laboratories, 16 Divinity Ave, Harvard University, Cambridge, MA 02138, USA
    J Bacteriol 187:6641-50. 2005
    ..The antitoxin, which is called RatA (for RNA antitoxin A), is a small (222 nucleotides), untranslated RNA that blocks the accumulation of the mRNA for a toxic peptide TxpA (for toxic peptide A; formerly YqdB)...
  51. ncbi The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli
    M Y Liu
    Department of Microbiology and Immunology, University of North Texas Health Science Center at Fort Worth, Fort Worth, Texas 76107 2699, USA
    J Biol Chem 272:17502-10. 1997
    ..A highly repeated nucleotide sequence located within predicted stem-loops and other single-stranded regions of CsrB, CAGGA(U/A/C)G, is a plausible CsrA-binding element...
  52. ncbi Epimutation of the telomeric imprinting center region on chromosome 11p15 in Silver-Russell syndrome
    Christine Gicquel
    Laboratoire d Explorations Fonctionnelles Endocriniennes, Inserm U515 et UPMC Paris 6, Hopital Armand Trousseau, AP HP, 26 Avenue Arnold Netter, 75012 Paris, France
    Nat Genet 37:1003-7. 2005
    ..These findings provide new insight into the pathogenesis of SRS and strongly suggest that the 11p15 imprinted region, in addition to those of 7p11.2-p13 and 7q31-qter, is involved in SRS...
  53. pmc Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    Ryan Lister
    Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 133:523-36. 2008
    ..Finally, strand-specific mRNA-seq revealed altered transcript abundance of hundreds of genes, transposons, and unannotated intergenic transcripts upon modification of the DNA methylation state...
  54. ncbi Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms
    John S Mattick
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia
    Bioessays 25:930-9. 2003
    ..This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoietic development and phenotypic variation...
  55. pmc The genetic signatures of noncoding RNAs
    John S Mattick
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    PLoS Genet 5:e1000459. 2009
    ..There is every possibility that many of these variations will alter the interactions between regulatory RNAs and their targets, a prospect that should be borne in mind in future functional analyses...
  56. pmc A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
    Thomas Geissmann
    Architecture et Reactivite de l ARN, Universite de Strasbourg, CNRS, IBMC, 15 rue Rene Descartes, F 67084 Strasbourg, France
    Nucleic Acids Res 37:7239-57. 2009
    ..This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism...
  57. ncbi Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation
    E Heard
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Cell 107:727-38. 2001
    ..We also identify a unique "hotspot" of H3 Lys-9 methylation 5' to Xist, and we propose that this acts as a nucleation center for Xist RNA-dependent spread of inactivation along the X chromosome via H3 Lys-9 methylation...
  58. ncbi A rough guide to the non-coding RNA world of Salmonella
    Jörg Vogel
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 71:1-11. 2009
    ....
  59. ncbi Regulation of RpoS by a novel small RNA: the characterization of RprA
    N Majdalani
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bldg 37 Room 2E 18, Bethesda, MD 20892 4255, USA
    Mol Microbiol 39:1382-94. 2001
    ..The existence of two very different small RNA regulators of RpoS translation suggests that such additional regulatory RNAs are likely to exist, both for regulation of RpoS and for regulation of other important cellular components...
  60. ncbi Non-coding RNAs: hope or hype?
    Alexander Huttenhofer
    Division of Genomics and RNomics, Innsbruck Medical University Biocenter, Fritz Pregl Strasse 3, 6020 Innsbruck, Austria
    Trends Genet 21:289-97. 2005
    ....
  61. ncbi Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
    Joseph A Martens
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 429:571-4. 2004
    ..This work identifies a previously unknown class of transcriptional regulatory genes...
  62. pmc Accumulation of miR-155 and BIC RNA in human B cell lymphomas
    Peggy S Eis
    Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 102:3627-32. 2005
    ..Because patients with activated B cell-type DLBCL have a poorer clinical prognosis, quantification of this microRNA may be diagnostically useful...
  63. pmc The C-terminal domain of Escherichia coli Hfq is required for regulation
    Branislav Vecerek
    Max F Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, 1030 Vienna, Austria
    Nucleic Acids Res 36:133-43. 2008
    ..These studies indicate that the C-terminal extension of E. coli Hfq constitutes a hitherto unrecognized RNA interaction surface with specificity for mRNAs...
  64. ncbi RNA-mediated response to heat shock in mammalian cells
    Ilya Shamovsky
    Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA
    Nature 440:556-60. 2006
    ..The central role of HSR1 during heat shock implies that targeting this RNA could serve as a new therapeutic model for cancer, inflammation and other conditions associated with HSF1 deregulation...
  65. pmc Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    Alexandra Sittka
    Max Planck Institute for Infection Biology, RNA Biology, Berlin, Germany
    PLoS Genet 4:e1000163. 2008
    ..We present a generic strategy that is ideal for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria...
  66. pmc 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA
    Jeremy E Wilusz
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Cell 135:919-32. 2008
    ..Our findings reveal a 3' end processing mechanism by which a single gene locus can yield both a stable nuclear-retained noncoding RNA with a short poly(A) tail-like moiety and a small tRNA-like cytoplasmic RNA...
  67. pmc MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles
    Yasnory T F Sasaki
    Functional RNomics Team, Biomedicinal Information Research Center, Tokyo 135 0064, Japan
    Proc Natl Acad Sci U S A 106:2525-30. 2009
    ..We postulate a model for nuclear paraspeckle body organization where specific ncRNAs and RNA-binding proteins cooperate to maintain and, presumably, establish the structure...
  68. ncbi A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 66:1174-91. 2007
    ..This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI-1 gene expression...
  69. pmc Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
    Ana C Marques
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, UK
    Genome Biol 10:R124. 2009
    ..This apparent difference may account for the surprisingly small fraction (11%) of transcripts that are represented in both catalogues. Here we sought to resolve the reported discrepancy between the evolutionary rates for these two sets...
  70. pmc The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA
    Toby J Soper
    Program in Cellular, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 2685, USA
    RNA 14:1907-17. 2008
    ..Once base-pairing between DsrA and rpoS mRNA is established, interactions between Hfq and the mRNA may stabilize the RNA complex by removing Hfq from the sRNA...
  71. ncbi RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli
    Jean François Jacques
    Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Groupe ARN Université de Sherbrooke, Sherbrooke, Quebec, Canada
    Mol Microbiol 62:1181-90. 2006
    ..Overall, our data demonstrate that, by regulating synthesis of nonessential iron-using proteins, the small RNA RyhB ensures that the iron is directed towards the iron-requiring enzymes that are indispensable...
  72. ncbi Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    Y Okazaki
    1 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nature 420:563-73. 2002
    ..The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics...
  73. pmc Antisense transcripts are targets for activating small RNAs
    Jacob C Schwartz
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9041, USA
    Nat Struct Mol Biol 15:842-8. 2008
    ..Our data demonstrate that antisense transcripts have a central role in recognition of the PR promoter by both activating and inhibitory agRNAs...
  74. pmc TargetRNA: a tool for predicting targets of small RNA action in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 36:W109-13. 2008
    ..The predictive performance of TargetRNA has been validated experimentally in several bacterial organisms. TargetRNA is freely available at http://snowwhite.wellesley.edu/targetRNA...
  75. ncbi Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs
    David P Bartel
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 5:396-400. 2004
  76. ncbi Xist-deficient mice are defective in dosage compensation but not spermatogenesis
    Y Marahrens
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 11:156-66. 1997
    The X-linked Xist gene encodes a large untranslated RNA that has been implicated in mammalian dosage compensation and in spermatogenesis...
  77. ncbi Characterization of the piRNA complex from rat testes
    Nelson C Lau
    Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
    Science 313:363-7. 2006
    ..Piwi has been genetically linked to TGS in flies, and slicer activity cofractionates with the purified complex. These results are consistent with a gene-silencing role for piRC in mammals...
  78. pmc A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster
    Xueqing Zhang
    Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
    Blood 113:2526-34. 2009
    ..These findings suggest that HOTAIRM1 plays a role in the myelopoiesis through modulation of gene expression in the HOXA cluster...
  79. pmc Evidence for a major role of antisense RNAs in cyanobacterial gene regulation
    Jens Georg
    Faculty of Biology and Freiburg Initiative in Systems Biology, University of Freiburg, Freiburg 79104, Germany
    Mol Syst Biol 5:305. 2009
    ..Extrapolated to the whole genome, approximately 10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks...
  80. ncbi Cohesin mediates transcriptional insulation by CCCTC-binding factor
    Kerstin S Wendt
    Research Institute of Molecular Pathology, Dr Bohr Gasse 7, 1030 Vienna, Austria
    Nature 451:796-801. 2008
    ..We propose that cohesin functions as a transcriptional insulator, and speculate that subtle deficiencies in this function contribute to 'cohesinopathies' such as Cornelia de Lange syndrome...
  81. ncbi CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae
    Derrick H Lenz
    Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544 1014, USA
    Mol Microbiol 58:1186-202. 2005
    ..The VarS/VarA-CsrA/BCD system converges with the V. cholerae quorum-sensing systems to regulate the expression of the Qrr sRNAs, and thus, the entire quorum-sensing regulon...
  82. pmc The H19 locus acts in vivo as a tumor suppressor
    Tomomi Yoshimizu
    Department of Genetics and Development, Institut Cochin, University Paris Descartes, Centre National de la Recherche Scientifique Unite Mixte de Recherche 8104, Institut National de la Sante et de la Recherche Medicale U567, Paris 75014, France
    Proc Natl Acad Sci U S A 105:12417-22. 2008
    ..The H19 locus thus clearly displays a tumor suppressor effect in mice...
  83. pmc Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator
    Thomas A Geissmann
    Institut Jacques Monod, CNRS Universités Paris 6 et Paris 7, Paris, France
    EMBO J 23:396-405. 2004
    ..Thus, Hfq is a critical chaperone in vivo and in vitro, changing the folding of the target mRNA to make it subject to the small RNA regulator...
  84. ncbi Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level
    Kai Papenfort
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Res Microbiol 160:278-87. 2009
    ..This review summarizes how and when several such regulators (CyaR, DsrA, GcvB, OmrAB, RNAIII, RybB, RyhB) act upon multiple targets...
  85. pmc Identification of small non-coding RNAs from mitochondria and chloroplasts
    Birgit Lung
    Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz Pregl Strasse 3, 6020 Innsbruck, Austria
    Nucleic Acids Res 34:3842-52. 2006
    ..The absence from our libraries of abundant small RNA species that are not encoded by the organellar genomes suggests that the import of RNAs into cell organelles is of very limited significance or does not occur at all...
  86. pmc XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure
    C M Clemson
    Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
    J Cell Biol 132:259-75. 1996
    ..XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging...
  87. ncbi The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus
    N Brockdorff
    Section of Comparative Biology, Medical Research Council Clinical Research Centre, Harrow, England
    Cell 71:515-26. 1992
    ..Together with conservation of inactive X-specific expression, these findings support a role for Xist in X inactivation, possibly as a functional RNA or as a chromatin organizer region...
  88. ncbi A microRNA in a multiple-turnover RNAi enzyme complex
    Gyorgy Hutvagner
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 825, 364 Plantation Street, Worcester, MA 01605, USA
    Science 297:2056-60. 2002
    ..Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells...
  89. ncbi CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
    A T Hark
    Howard Hughes Medical Institute and Department of Molecular Biology, Princeton University, New Jersey 08544, USA
    Nature 405:486-9. 2000
    ..Consistent with our model, CTCF binding is abolished by DNA methylation. This is the first example, to our knowledge, of a regulated chromatin boundary in vertebrates...
  90. pmc Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis
    Jessica M Silvaggi
    Department of Molecular and Cellular Biology, The Biological Laboratories, 16 Divinity Ave, Harvard University, Cambridge, MA 02138, USA
    J Bacteriol 188:532-41. 2006
    ..Our results indicate that the full repertoire of sporulation-specific gene expression involves the activation of multiple genes for small, noncoding RNAs...
  91. ncbi Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1
    Xiaoqin Fu
    Department of Surgery, Center for Prostate Disease Research CPDR, U S Military Cancer Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20852, USA
    DNA Cell Biol 25:135-41. 2006
    ..Further, these data unravel biological mechanisms of cell growth/cell survival-associated functions of this ncRNA in a widely used prostate cancer cell culture model...
  92. pmc Bidirectional promoters generate pervasive transcription in yeast
    Zhenyu Xu
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 457:1033-7. 2009
    ....
  93. ncbi An RNA gene expressed during cortical development evolved rapidly in humans
    Katherine S Pollard
    Center for Biomolecular Science and Engineering, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
    Nature 443:167-72. 2006
    ..HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology...
  94. pmc Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase
    Mohammad Ali Faghihi
    Molecular and Integrative Neurosciences Department, The Scripps Research Institute, 5353 Parkside Drive, Jupiter, Florida 33458, USA
    Nat Med 14:723-30. 2008
    ..In summary, we report that a long noncoding RNA is directly implicated in the increased abundance of Abeta 1-42 in Alzheimer's disease...
  95. ncbi Tsix silences Xist through modification of chromatin structure
    Takashi Sado
    Division of Human Genetics, National Institute of Genetics, Research Organization of Information and Systems, Japan
    Dev Cell 9:159-65. 2005
    ..Moreover, we show that disruption of Tsix impairs establishment of repressive epigenetic modifications and chromatin structure at the Xist locus. We propose that Tsix silences Xist through modification of the chromatin structure...
  96. pmc Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation
    Pablo Navarro
    Unité de Génétique Moléculaire Murine, URA 2578, Pasteur Institute, 75724 Paris Cedex 15, France
    Genes Dev 19:1474-84. 2005
    ..In this model, Tsix, by resetting the epigenetic state of the Xist/Tsix locus, mediates the transition from imprinted to random XCI...
  97. pmc Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation
    G Csankovszki
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    J Cell Biol 153:773-84. 2001
    ....
  98. ncbi Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch
    Mary E Donohoe
    Howard Hughes Medical Institute, USA
    Mol Cell 25:43-56. 2007
    ..Yy1 and Ctcf associate through specific protein-protein interactions and together transactivate Tsix. We propose that the Ctcf-Yy1-Tsix complex functions as a key component of the X chromosome binary switch...
  99. pmc Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription
    Helder I Nakaya
    Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
    Genome Biol 8:R43. 2007
    ..However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known...
  100. pmc Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB
    Taras Afonyushkin
    Max F Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter Dr Bohrgasse 9 4, A 1030 Vienna, Austria
    Nucleic Acids Res 33:1678-89. 2005
    ..These data are discussed in terms of a model, which accounts for the observed roles of RNase E and RNase III in sodB mRNA turnover...
  101. ncbi Regulation and mode of action of the second small RNA activator of RpoS translation, RprA
    Nadim Majdalani
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4264, USA
    Mol Microbiol 46:813-26. 2002
    ..This work suggests a new signal for RpoS translation and extends the global regulation effected by the RcsC/RcsB system to coregulation of RpoS with capsule and FtsZ...

Research Grants66

  1. FOXP3-microRNA146-NFkB Axis in Tumor Suppression
    Lizhong Wang; Fiscal Year: 2013
    ..abstract_text> ..
  2. Viral And host mechanisms that tilt the HSV lytic/latent balance
    Donald M Coen; Fiscal Year: 2013
    ..This research wil define basic mechanisms of herpes simplex virus latent infection and new targets for potential drugs to treat the latent infection of these viruses. ..
  3. Epigenetic Changes in the Glucocorticoid Receptor Gene Due to Arsenic Exposure
    Andrea M Allan; Fiscal Year: 2013
    ..Our investigation will use a prenatal arsenic-exposed mouse model to explore the epigenetic changes to the expression of the glucocorticoid receptor gene. ..
  4. Noncoding RNA targets of the spinal muscular atrophy protein
    Livio Pellizzoni; Fiscal Year: 2010
    ..These studies have the potential to provide unanticipated insights into the molecular mechanisms of SMA and to suggest new avenues of therapeutic intervention. ..
  5. Generating Blood-based Diagnosis for Alzheimer Disease
    Eugenia Wang; Fiscal Year: 2012
    ..being the first such AD diagnostic, indicating not only disease presence, but also its progress (and even drug efficacy monitoring), a huge strate- gic gain for the victims of this costly disease, and our society at large! ..
  6. Catalytic inactivation of miRNA function by customized RNase P-based ribozymes
    DANIEL R contact SCHOENBERG; Fiscal Year: 2010
    ..This proposal describes a new approach to inactivating miR-122 using a catalytic RNA enzyme. The long term goal is to apply this strategy to the treatment of HCV infection. ..
  7. NEUROSECRETORY GENE EXPRESSION IN THE HYPOTHALAMUS
    Pamela L Mellon; Fiscal Year: 2013
    ..This multifaceted approach should yield a comprehensive understanding of the program of GnRH neuronal migration and cell fate in vivo and in vitro and provide insight into the genetics of hypogonadotropic hypogonadism. ..
  8. RNA quality control and environmental stress
    Sandra L Wolin; Fiscal Year: 2013
    ....
  9. Chromatin and Herpes Simplex Virus Latency
    David M Knipe; Fiscal Year: 2013
    ....
  10. Rescue of developmental disorders in utero by gene-specific small molecules
    Michael J Higgins; Fiscal Year: 2011
    ..These studies will highlight the utility of these drugs in the treatment of a wide variety of human diseases. ..
  11. Prostate Cancer Detection by Molecular Urinalysis
    Christian P Pavlovich; Fiscal Year: 2010
    ..Hopefully, useful biomarker information for prostate cancer will also result from my period of study. ..
  12. Polycomb complexes targeted to specific loci by non-coding RNA co-factors
    Jeannie T Lee; Fiscal Year: 2013
    ....
  13. MicroRNA-mediated regulation of ATG16L1 expression and autophagy
    John Kwon; Fiscal Year: 2012
    ....
  14. The Role of microRNA Alterations in Barrett's Carcinogenesis
    Stephen J Meltzer; Fiscal Year: 2012
    ..In this fashion, we will gain comprehensive insights into the molecular basis of BEAN, while simultaneously establishing a foundation for future potential predictive and diagnostic assays and therapeutic intervention strategies. ..
  15. Regulation of noncoding RNA biogenesis and function
    JEREMY WILUSZ; Fiscal Year: 2013
    ....
  16. Identify and characterize genes involved in X-chromosome inactivation
    Zhiguo Zhang; Fiscal Year: 2013
    ....
  17. A role for microRNAs in global changes in gene expression induced by Leishmania
    MARY EDYTHE WILSON; Fiscal Year: 2010
    ..Future goals of this research include the use of microRNAs to develop novel targets for treatment of human leishmaniasis. ..
  18. Investigation of a Novel Role for RNA Binding Proteins in DNA Repair
    William S Dynan; Fiscal Year: 2013
    ....
  19. Altered miRNA expression in mesangial cells in lupus mice
    CHRISTOPHER MICHAEL REILLY; Fiscal Year: 2011
    ..If we can establish a role for altered miRNA expression in lupus, these studies will shift the paradigm in our understanding of how SLE disease is initiated. ..
  20. MECHANISMS FOR REARRANGING RNA DURING PRE-MRNA SPLICING
    Jonathan P Staley; Fiscal Year: 2013
    ..A major goal of our work is to determine how errors in this process are prevented to better understand the etiology of disease and how to treat disease. ..
  21. The Biology and Biochemistry of ADAR RNA Editing Enzymes
    Brenda L Bass; Fiscal Year: 2013
    ..After validation of observations made with bioinformatics studies, phenotypes suggested by molecular defects will be tested. ..
  22. Mechanisms of Epstein-Barr Virus Persistence
    Jeffery T Sample; Fiscal Year: 2013
    ..Finally, in Aim 3 we will characterize and explore the contribution to EBV latency of a family of novel RNA transcripts that span the EBNA promoter Cp. ..
  23. Heterochromatin instability and misregulation of noncoding RNA in cancer
    Dawn M Carone; Fiscal Year: 2013
    ..Over the longer-term, the robust "satellite RNA signature" observed within cancer samples may serve as a biomarker for early detection and prognosis of cancer. ..
  24. Role of Noncoding RNAs in Epidermal Differentiation
    BRYAN SUN; Fiscal Year: 2012
    ....
  25. NsrR regulation of the small noncoding RNA RybB in Escherichia coli
    Karl M Thompson; Fiscal Year: 2013
    ..The models resulting from these studies will contribute to refined physiological models for systems biology applications. ..
  26. New Players in Urethral Closure;Defining the Role of a Novel Long Noncoding RNA
    Andrew J Pask; Fiscal Year: 2013
    ....
  27. Regulation of transcription by the RNA-binding protein FUS
    Jacob C Schwartz; Fiscal Year: 2013
    ..Completion of this study will provide a list of genes regulated by FUS, solidify a mechanism for the RNA-directed recruitment of FUS and demonstrate how these interactions are required for FUS activity in cells. ..
  28. Regulatory RNAs as mediators and biomarkers in Alzheimer's Disease
    CLAES ROBERT WAHLESTEDT; Fiscal Year: 2012
    ..Understanding the mechanisms by which BACE1 is regulated may reveal important insights into the pathogenesis of AD, and lead to the development of novel therapeutics and AD biomarkers. ..
  29. Role of noncoding RNA in Regulating GVHD
    Pavan Reddy; Fiscal Year: 2013
    ..Such an approach may prove to be beneficial in a broad array of many other T cell mediated immune diseases. ..
  30. Transcriptional Regulators in Normal Human Brain Development and Autism
    NEELROOP NARENDRA PARIKSHAK; Fiscal Year: 2012
    ..It will combine neuroscience, genetics, and bioinformatics, to systematically identify molecules that regulate gene expression in functional molecular pathways that may be potential therapeutic targets in ASD. ..
  31. EPIGENETIC REGULATION IN A CANCER ASSOCIATED REGION
    Michael J Higgins; Fiscal Year: 2012
    ..abstract_text> ..
  32. Mechanism of Gene Regulation by RNA-Binding ANTAR Proteins
    Wade Winkler; Fiscal Year: 2011
    ..that an activated two-component system (TCS) and adenosylcobalamin (AdoCbl) bind to specific regions in the untranslated RNA (UTR) of the ethanolamine utilization operon (eut) operon proximal to predicted terminators preventing their ..
  33. A role for the miroRNA miR-133b in synapse development
    MARY PATRICIA HEYER; Fiscal Year: 2010
    ..This work will deepen our understanding of the complexities of synapse development, with future relevance for central synaptic disorders, which are of significant concern for public health. ..
  34. Antisense RNA Mediated Epigenetic Regulation of Brain Derived Neurotrophic Factor
    Mohammad Ali Faghihi; Fiscal Year: 2013
    ..Overall these projects will pave the road for future epigenetic studies on other genomic loci, serving to establish novel noncoding RNA therapeutic targets for several neuropsychological disorders. ..
  35. The Role of Long Non-coding RNAs in Lineage Restriction of Neural Stem Cells
    ALEXANDER DANIEL RAMOS; Fiscal Year: 2013
    ..I hypothesize that Dlx1as is required for neurogenesis in vivo through modulation of the chromatin- modifying factors recruited to the Dlx1/2 locus. ..
  36. Ligand Regulated Epigenetic/Nuclear Architectural Strategies and Human Disease
    Michael G Rosenfeld; Fiscal Year: 2013
    ..We suggest that these mechanisms are likely to provide important insights, and possibly new intervention strategies, into many human diseases, including neurodegeneration, defects of development, diabetes and cancer. ..
  37. RNA-Gain-of-Function Pathogenesis in SCA10
    Tetsuo Ashizawa; Fiscal Year: 2013
    ..We showed that the untranslated RNA transcript of the expanded repeat is accumulated in intracellular foci and interacts with heterogeneous ..
  38. Mechanisms Underlying Regulation of Non-Coding RNA Transcription
    BRETT NEUMAN TOMSON; Fiscal Year: 2012
    ..abstract_text> ..
  39. Macrophage-Activating MicroRNAs In the Pathogenesis of Leishmaniasis
    Mary E Wilson; Fiscal Year: 2013
    ..abstract_text> ..
  40. GENETICS OF HYPERTENSION
    Bina Joe; Fiscal Year: 2013
    ....
  41. PROCESSING AND FUNCTION OF POLYOMA RNA
    Gordon G Carmichael; Fiscal Year: 2013
    ....
  42. Noncoding RNAs at the heart of the Prader-Willi locus
    Janine M LaSalle; Fiscal Year: 2013
    ..The results of these experiments are expected to improve understanding of functional role of the lncRNAs at the heart of the PWS locus and potentially enable future epigenetic therapies for PWS. ..
  43. Mapping adiposity genes in mice
    DANIELLE RENEE REED; Fiscal Year: 2013
    ..The long-range goal of this work is to develop an approach to systematically identify genes that contribute to normal variation in fatness among mice. ..
  44. Corneal HSV-1: LAT's Anti-Apoptosis Activity and Latency
    Steven L Wechsler; Fiscal Year: 2013
    ..abstract_text> ..
  45. REGULATION BY THE ESCHERICHIA COLI SMALL RNA, DSRA
    DARREN SLEDJESKI; Fiscal Year: 2002
    DsrA is a small, stable, untranslated RNA that is conserved between Escherichia coli, Klebsiella pneumoniae, and Salmonella typhimurium. DsrA RNA regulates two different global regulatory networks...
  46. Genetics of Type 2 Diabetes
    Steven C Elbein; Fiscal Year: 2010
    ....
  47. Resolving MicroRNA Targets
    Michael T McManus; Fiscal Year: 2010
    ..However, little is known about how this works, and what are the genes involved. This proposal describes our efforts to develop novel methods for interrogating the biology of small RNAs in the brain. ..
  48. Noncoding RNA Regulators of Epithelial Homeostasis and Neoplasia
    CAROLYN S LEE; Fiscal Year: 2012
    ..S. population, including skin cancers and chronic wounds. The current efforts are designed to yield insight and targets to aid in the development of future therapies for these disorders. ..
  49. Roles of Pif1 family helicases in Genomic Integrity and Telomere Maintenance
    JENNIFER LEIGH STUNDON; Fiscal Year: 2013
    ..2007. Science. 318: 798-801 Bochman, M.L., Sabouri, N., Zakian, V.A. 2010. Unwinding the functions of the Pif1 family of helicases. DNA Repair. (9):3 237-249. ..
  50. Coordinated regulation of floral transition by protein and long ncRNA components
    Sibum Sung; Fiscal Year: 2013
    ..e. flowering) but also for elucidating the mechanism of epigenetic regulation of gene expression which has a deep evolutionary root among eukaryotes. ..
  51. Identification and characterization of long noncoding RNAs in human melanomas
    RANJAN JOSEPH PERERA; Fiscal Year: 2013
    ..The proposed study has the potential to have a high-impact on our understanding of melanoma development. ..
  52. Signaling Regulators of Epithelial Homeostasis and Neoplasia
    Paul A Khavari; Fiscal Year: 2013
    ..We are characterizing the role of proteins that interact with the Erk MAPK pathway and of novel noncoding RNA targets that may mediate its broad gene regulatory effects in normal and cancerous epidermis. ..
  53. Noncoding RNAs in Development and Cancer
    JAMES WAVELL AIKEN; Fiscal Year: 2013
    ....
  54. System and Methods for Analysis of Bacterial Transcriptomes
    Brian Tjaden; Fiscal Year: 2013
    ..The methods developed will be applied and evaluated in several different bacterial systems. ..
  55. STRUCTURE/FUNCTION RELATIONS IN HAV REPLICATION
    STANLEY LEMON; Fiscal Year: 2000
    ..The long-term goals of these studies are an improved understanding of the cap-independent initiation of translation by picornaviral 5NTRs and the development of new attenuated hepatitis A vaccine candidates. ..
  56. 2009 Epigenetics Gordon Research Conference
    JEANNIE LEE; Fiscal Year: 2009
    ....
  57. Mechanisms of decay of toxic CUGn RNA in DM1 patients
    Lubov Timchenko; Fiscal Year: 2009
    ..We and others found that DM1 mutation causes a disease through accumulation of untranslated RNA CUG repeats which disrupt RNA processing in patients'cells...
  58. The Mechanism of Heat Shock Activation
    Evgeny Nudler; Fiscal Year: 2007
    ..of HSF 1 requires at least two associated factors: a translation elongation factor EF- 1A and novel untranslated RNA (HSR)...
  59. Differential Expression and Regulatory Functions of Long Non-Coding RNA Molecules
    Leonard Lipovich; Fiscal Year: 2009
    ....
  60. XIST RNA and Ovarian Cancer
    Shu wing Ng; Fiscal Year: 2005
    ....
  61. Biogenesis of Small RNAs
    SANDRA WOLIN; Fiscal Year: 2009
    ..By understanding these processes, it may be possible to design treatments for diseases caused by noncoding RNAs that do not function properly. ..
  62. BASIS FOR THE IFP PHENOTYPE OF DIABETOGENIC EMC VIRUS
    GEORGE JORDAN; Fiscal Year: 1990
    ..Also, the first 103 nucleotides of the untranslated RNA at the 5' end of the genomes are identical...
  63. MHC suppression as a model for transplant tolerance
    Arnar Geirsson; Fiscal Year: 2007
    ..Long waiting times and ethical dilemmas regarding organ allocation to patients with end stage organ disease is now a pressing medical dilemma. [unreadable] [unreadable] [unreadable]..
  64. Methods for characterizing noncoding RNAs in bacteria
    Brian Tjaden; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  65. INHIBITION OF BREAST TUMORIGENICITY BY C MYC PO RNA
    SCOTT BLUME; Fiscal Year: 2002
    ..We hypothesize that this 5'-untranslated RNA sequence is a fundamental participant in the transcriptional regulation of c-myc and the ultimate ..
  66. Characterization of noncoding RNA by functional genomics
    AARRON WILLINGHAM; Fiscal Year: 2005
    ..Further examination will define their regulatory relationship and biological significance. ..